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lib/queries/biological_association/filter.rb

Summary

Maintainability
F
3 days
Test Coverage

Possible SQL injection
Open

            '(' + [a,b].compact.collect{|q| '(' + q.to_sql + ')'}.join(' UNION ') + ') as biological_associations'
Severity: Minor
Found in lib/queries/biological_association/filter.rb by brakeman

Injection is #1 on the 2013 OWASP Top Ten web security risks. SQL injection is when a user is able to manipulate a value which is used unsafely inside a SQL query. This can lead to data leaks, data loss, elevation of privilege, and other unpleasant outcomes.

Brakeman focuses on ActiveRecord methods dealing with building SQL statements.

A basic (Rails 2.x) example looks like this:

User.first(:conditions => "username = '#{params[:username]}'")

Brakeman would produce a warning like this:

Possible SQL injection near line 30: User.first(:conditions => ("username = '#{params[:username]}'"))

The safe way to do this query is to use a parameterized query:

User.first(:conditions => ["username = ?", params[:username]])

Brakeman also understands the new Rails 3.x way of doing things (and local variables and concatenation):

username = params[:user][:name].downcase
password = params[:user][:password]

User.first.where("username = '" + username + "' AND password = '" + password + "'")

This results in this kind of warning:

Possible SQL injection near line 37:
User.first.where((((("username = '" + params[:user][:name].downcase) + "' AND password = '") + params[:user][:password]) + "'"))

See the Ruby Security Guide for more information and Rails-SQLi.org for many examples of SQL injection in Rails.

Possible SQL injection
Open

            '(' + [a,b].compact.collect{|q| '(' + q.to_sql + ')'}.join(' INTERSECT ') + ') as biological_associations'
Severity: Minor
Found in lib/queries/biological_association/filter.rb by brakeman

Injection is #1 on the 2013 OWASP Top Ten web security risks. SQL injection is when a user is able to manipulate a value which is used unsafely inside a SQL query. This can lead to data leaks, data loss, elevation of privilege, and other unpleasant outcomes.

Brakeman focuses on ActiveRecord methods dealing with building SQL statements.

A basic (Rails 2.x) example looks like this:

User.first(:conditions => "username = '#{params[:username]}'")

Brakeman would produce a warning like this:

Possible SQL injection near line 30: User.first(:conditions => ("username = '#{params[:username]}'"))

The safe way to do this query is to use a parameterized query:

User.first(:conditions => ["username = ?", params[:username]])

Brakeman also understands the new Rails 3.x way of doing things (and local variables and concatenation):

username = params[:user][:name].downcase
password = params[:user][:password]

User.first.where("username = '" + username + "' AND password = '" + password + "'")

This results in this kind of warning:

Possible SQL injection near line 37:
User.first.where((((("username = '" + params[:user][:name].downcase) + "' AND password = '") + params[:user][:password]) + "'"))

See the Ruby Security Guide for more information and Rails-SQLi.org for many examples of SQL injection in Rails.

Possible SQL injection
Open

        return ::BiologicalAssociation.from('(' + s + ') as biological_associations')
Severity: Minor
Found in lib/queries/biological_association/filter.rb by brakeman

Injection is #1 on the 2013 OWASP Top Ten web security risks. SQL injection is when a user is able to manipulate a value which is used unsafely inside a SQL query. This can lead to data leaks, data loss, elevation of privilege, and other unpleasant outcomes.

Brakeman focuses on ActiveRecord methods dealing with building SQL statements.

A basic (Rails 2.x) example looks like this:

User.first(:conditions => "username = '#{params[:username]}'")

Brakeman would produce a warning like this:

Possible SQL injection near line 30: User.first(:conditions => ("username = '#{params[:username]}'"))

The safe way to do this query is to use a parameterized query:

User.first(:conditions => ["username = ?", params[:username]])

Brakeman also understands the new Rails 3.x way of doing things (and local variables and concatenation):

username = params[:user][:name].downcase
password = params[:user][:password]

User.first.where("username = '" + username + "' AND password = '" + password + "'")

This results in this kind of warning:

Possible SQL injection near line 37:
User.first.where((((("username = '" + params[:user][:name].downcase) + "' AND password = '") + params[:user][:password]) + "'"))

See the Ruby Security Guide for more information and Rails-SQLi.org for many examples of SQL injection in Rails.

Possible SQL injection
Open

            .joins("JOIN b_objects as b_objects1 on b_objects1.id = biological_associations.biological_association_object_id AND biological_associations.biological_association_object_type = '" + target + "'")
Severity: Minor
Found in lib/queries/biological_association/filter.rb by brakeman

Injection is #1 on the 2013 OWASP Top Ten web security risks. SQL injection is when a user is able to manipulate a value which is used unsafely inside a SQL query. This can lead to data leaks, data loss, elevation of privilege, and other unpleasant outcomes.

Brakeman focuses on ActiveRecord methods dealing with building SQL statements.

A basic (Rails 2.x) example looks like this:

User.first(:conditions => "username = '#{params[:username]}'")

Brakeman would produce a warning like this:

Possible SQL injection near line 30: User.first(:conditions => ("username = '#{params[:username]}'"))

The safe way to do this query is to use a parameterized query:

User.first(:conditions => ["username = ?", params[:username]])

Brakeman also understands the new Rails 3.x way of doing things (and local variables and concatenation):

username = params[:user][:name].downcase
password = params[:user][:password]

User.first.where("username = '" + username + "' AND password = '" + password + "'")

This results in this kind of warning:

Possible SQL injection near line 37:
User.first.where((((("username = '" + params[:user][:name].downcase) + "' AND password = '") + params[:user][:password]) + "'"))

See the Ruby Security Guide for more information and Rails-SQLi.org for many examples of SQL injection in Rails.

Possible SQL injection
Open

            .joins("JOIN a_#{target}_objects as a_#{target}_objects1 on a_#{target}_objects1.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'Otu'").to_sql
Severity: Minor
Found in lib/queries/biological_association/filter.rb by brakeman

Injection is #1 on the 2013 OWASP Top Ten web security risks. SQL injection is when a user is able to manipulate a value which is used unsafely inside a SQL query. This can lead to data leaks, data loss, elevation of privilege, and other unpleasant outcomes.

Brakeman focuses on ActiveRecord methods dealing with building SQL statements.

A basic (Rails 2.x) example looks like this:

User.first(:conditions => "username = '#{params[:username]}'")

Brakeman would produce a warning like this:

Possible SQL injection near line 30: User.first(:conditions => ("username = '#{params[:username]}'"))

The safe way to do this query is to use a parameterized query:

User.first(:conditions => ["username = ?", params[:username]])

Brakeman also understands the new Rails 3.x way of doing things (and local variables and concatenation):

username = params[:user][:name].downcase
password = params[:user][:password]

User.first.where("username = '" + username + "' AND password = '" + password + "'")

This results in this kind of warning:

Possible SQL injection near line 37:
User.first.where((((("username = '" + params[:user][:name].downcase) + "' AND password = '") + params[:user][:password]) + "'"))

See the Ruby Security Guide for more information and Rails-SQLi.org for many examples of SQL injection in Rails.

Possible SQL injection
Open

            .joins("LEFT JOIN a_objects as a_objects1 on a_objects1.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = '" + target + "'")
Severity: Minor
Found in lib/queries/biological_association/filter.rb by brakeman

Injection is #1 on the 2013 OWASP Top Ten web security risks. SQL injection is when a user is able to manipulate a value which is used unsafely inside a SQL query. This can lead to data leaks, data loss, elevation of privilege, and other unpleasant outcomes.

Brakeman focuses on ActiveRecord methods dealing with building SQL statements.

A basic (Rails 2.x) example looks like this:

User.first(:conditions => "username = '#{params[:username]}'")

Brakeman would produce a warning like this:

Possible SQL injection near line 30: User.first(:conditions => ("username = '#{params[:username]}'"))

The safe way to do this query is to use a parameterized query:

User.first(:conditions => ["username = ?", params[:username]])

Brakeman also understands the new Rails 3.x way of doing things (and local variables and concatenation):

username = params[:user][:name].downcase
password = params[:user][:password]

User.first.where("username = '" + username + "' AND password = '" + password + "'")

This results in this kind of warning:

Possible SQL injection near line 37:
User.first.where((((("username = '" + params[:user][:name].downcase) + "' AND password = '") + params[:user][:password]) + "'"))

See the Ruby Security Guide for more information and Rails-SQLi.org for many examples of SQL injection in Rails.

Possible SQL injection
Open

          '(' + [d,e].compact.collect{|q| '(' + q + ')'}.join(' UNION ') + ') as biological_associations'
Severity: Minor
Found in lib/queries/biological_association/filter.rb by brakeman

Injection is #1 on the 2013 OWASP Top Ten web security risks. SQL injection is when a user is able to manipulate a value which is used unsafely inside a SQL query. This can lead to data leaks, data loss, elevation of privilege, and other unpleasant outcomes.

Brakeman focuses on ActiveRecord methods dealing with building SQL statements.

A basic (Rails 2.x) example looks like this:

User.first(:conditions => "username = '#{params[:username]}'")

Brakeman would produce a warning like this:

Possible SQL injection near line 30: User.first(:conditions => ("username = '#{params[:username]}'"))

The safe way to do this query is to use a parameterized query:

User.first(:conditions => ["username = ?", params[:username]])

Brakeman also understands the new Rails 3.x way of doing things (and local variables and concatenation):

username = params[:user][:name].downcase
password = params[:user][:password]

User.first.where("username = '" + username + "' AND password = '" + password + "'")

This results in this kind of warning:

Possible SQL injection near line 37:
User.first.where((((("username = '" + params[:user][:name].downcase) + "' AND password = '") + params[:user][:password]) + "'"))

See the Ruby Security Guide for more information and Rails-SQLi.org for many examples of SQL injection in Rails.

Possible SQL injection
Open

            .joins("LEFT JOIN a_objects as a_objects1 on a_objects1.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = '" + target + "'")
Severity: Minor
Found in lib/queries/biological_association/filter.rb by brakeman

Injection is #1 on the 2013 OWASP Top Ten web security risks. SQL injection is when a user is able to manipulate a value which is used unsafely inside a SQL query. This can lead to data leaks, data loss, elevation of privilege, and other unpleasant outcomes.

Brakeman focuses on ActiveRecord methods dealing with building SQL statements.

A basic (Rails 2.x) example looks like this:

User.first(:conditions => "username = '#{params[:username]}'")

Brakeman would produce a warning like this:

Possible SQL injection near line 30: User.first(:conditions => ("username = '#{params[:username]}'"))

The safe way to do this query is to use a parameterized query:

User.first(:conditions => ["username = ?", params[:username]])

Brakeman also understands the new Rails 3.x way of doing things (and local variables and concatenation):

username = params[:user][:name].downcase
password = params[:user][:password]

User.first.where("username = '" + username + "' AND password = '" + password + "'")

This results in this kind of warning:

Possible SQL injection near line 37:
User.first.where((((("username = '" + params[:user][:name].downcase) + "' AND password = '") + params[:user][:password]) + "'"))

See the Ruby Security Guide for more information and Rails-SQLi.org for many examples of SQL injection in Rails.

Possible SQL injection
Open

            .joins("JOIN a_objects as a_objects1 on a_objects1.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = '" + target + "'")
Severity: Minor
Found in lib/queries/biological_association/filter.rb by brakeman

Injection is #1 on the 2013 OWASP Top Ten web security risks. SQL injection is when a user is able to manipulate a value which is used unsafely inside a SQL query. This can lead to data leaks, data loss, elevation of privilege, and other unpleasant outcomes.

Brakeman focuses on ActiveRecord methods dealing with building SQL statements.

A basic (Rails 2.x) example looks like this:

User.first(:conditions => "username = '#{params[:username]}'")

Brakeman would produce a warning like this:

Possible SQL injection near line 30: User.first(:conditions => ("username = '#{params[:username]}'"))

The safe way to do this query is to use a parameterized query:

User.first(:conditions => ["username = ?", params[:username]])

Brakeman also understands the new Rails 3.x way of doing things (and local variables and concatenation):

username = params[:user][:name].downcase
password = params[:user][:password]

User.first.where("username = '" + username + "' AND password = '" + password + "'")

This results in this kind of warning:

Possible SQL injection near line 37:
User.first.where((((("username = '" + params[:user][:name].downcase) + "' AND password = '") + params[:user][:password]) + "'"))

See the Ruby Security Guide for more information and Rails-SQLi.org for many examples of SQL injection in Rails.

Possible SQL injection
Open

            .joins("JOIN b_#{target}_objects as b_#{target}_objects1 on b_#{target}_objects1.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'CollectionObject'").to_sql
Severity: Minor
Found in lib/queries/biological_association/filter.rb by brakeman

Injection is #1 on the 2013 OWASP Top Ten web security risks. SQL injection is when a user is able to manipulate a value which is used unsafely inside a SQL query. This can lead to data leaks, data loss, elevation of privilege, and other unpleasant outcomes.

Brakeman focuses on ActiveRecord methods dealing with building SQL statements.

A basic (Rails 2.x) example looks like this:

User.first(:conditions => "username = '#{params[:username]}'")

Brakeman would produce a warning like this:

Possible SQL injection near line 30: User.first(:conditions => ("username = '#{params[:username]}'"))

The safe way to do this query is to use a parameterized query:

User.first(:conditions => ["username = ?", params[:username]])

Brakeman also understands the new Rails 3.x way of doing things (and local variables and concatenation):

username = params[:user][:name].downcase
password = params[:user][:password]

User.first.where("username = '" + username + "' AND password = '" + password + "'")

This results in this kind of warning:

Possible SQL injection near line 37:
User.first.where((((("username = '" + params[:user][:name].downcase) + "' AND password = '") + params[:user][:password]) + "'"))

See the Ruby Security Guide for more information and Rails-SQLi.org for many examples of SQL injection in Rails.

File filter.rb has 567 lines of code (exceeds 250 allowed). Consider refactoring.
Open

module Queries
  module BiologicalAssociation

    class Filter < Query::Filter
      include Queries::Concerns::Notes
Severity: Major
Found in lib/queries/biological_association/filter.rb - About 1 day to fix

    Class Filter has 64 methods (exceeds 20 allowed). Consider refactoring.
    Open

        class Filter < Query::Filter
      include Queries::Concerns::Notes
      include Queries::Concerns::Tags
      include Queries::Concerns::Citations
      include Queries::Concerns::Depictions
    Severity: Major
    Found in lib/queries/biological_association/filter.rb - About 1 day to fix

      Method has too many lines. [32/25]
      Open

            def initialize(query_params)
        super

        @any_global_id = params[:any_global_id]
        @biological_association_id = params[:biological_association_id]
      Severity: Minor
      Found in lib/queries/biological_association/filter.rb by rubocop

      This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

      Method has too many lines. [26/25]
      Open

            def target_scope(target = 'subject')
        a = send((target + '_otu_query').to_sym)
        b = send((target + '_collection_object_query').to_sym)

        a_sql, b_sql = nil, nil
      Severity: Minor
      Found in lib/queries/biological_association/filter.rb by rubocop

      This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

      Method subject_object_scope has 38 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

            def subject_object_scope(subject_query, object_query, target = 'Otu')
        a = subject_query
        b = object_query

        a_sql, b_sql = nil, nil
      Severity: Minor
      Found in lib/queries/biological_association/filter.rb - About 1 hr to fix

        Method initialize has 32 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

              def initialize(query_params)
        super

        @any_global_id = params[:any_global_id]
        @biological_association_id = params[:biological_association_id]
        Severity: Minor
        Found in lib/queries/biological_association/filter.rb - About 1 hr to fix

          Method subject_object_scope has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
          Open

                def subject_object_scope(subject_query, object_query, target = 'Otu')
        a = subject_query
        b = object_query

        a_sql, b_sql = nil, nil
          Severity: Minor
          Found in lib/queries/biological_association/filter.rb - About 1 hr to fix

          Cognitive Complexity

          Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

          A method's cognitive complexity is based on a few simple rules:

          • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
          • Code is considered more complex for each "break in the linear flow of the code"
          • Code is considered more complex when "flow breaking structures are nested"

          Further reading

          Method target_scope has 26 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

                def target_scope(target = 'subject')
        a = send((target + '_otu_query').to_sym)
        b = send((target + '_collection_object_query').to_sym)

        a_sql, b_sql = nil, nil
          Severity: Minor
          Found in lib/queries/biological_association/filter.rb - About 1 hr to fix

            Method target_scope has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
            Open

                  def target_scope(target = 'subject')
        a = send((target + '_otu_query').to_sym)
        b = send((target + '_collection_object_query').to_sym)

        a_sql, b_sql = nil, nil
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb - About 45 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            Method any_global_id_facet has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
            Open

                  def any_global_id_facet
        return nil if any_global_id.empty?
        a = matching_global_id(:subject, any_global_id)
        b = matching_global_id(:object, any_global_id)
        if a && b
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb - About 35 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                  def asserted_distribution_query_facet
        return nil if asserted_distribution_query.nil?
        s = 'WITH query_ad_ba AS (' + asserted_distribution_query.all.to_sql + ') '

        a = ::BiologicalAssociation
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb and 2 other locations - About 40 mins to fix
            lib/queries/biological_association/filter.rb on lines 642..653
            lib/queries/biological_association/filter.rb on lines 670..682

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 37.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                  def collection_object_query_facet
        return nil if collection_object_query.nil?
        s = 'WITH query_co_ba AS (' + collection_object_query.all.to_sql + ') '

        a = ::BiologicalAssociation
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb and 2 other locations - About 40 mins to fix
            lib/queries/biological_association/filter.rb on lines 642..653
            lib/queries/biological_association/filter.rb on lines 656..667

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 37.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                  def otu_query_facet
        return nil if otu_query.nil?
        s = 'WITH query_otu_ba AS (' + otu_query.all.to_sql + ') '

        a = ::BiologicalAssociation
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb and 2 other locations - About 40 mins to fix
            lib/queries/biological_association/filter.rb on lines 656..667
            lib/queries/biological_association/filter.rb on lines 670..682

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 37.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                  def object_collection_object_query
        p = collection_object_params
        s = object_taxon_name_ids

        if p.blank? && s.empty? # .nil?
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb and 1 other location - About 25 mins to fix
            lib/queries/biological_association/filter.rb on lines 387..398

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 29.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                  def subject_collection_object_query
        p = collection_object_params
        s = subject_taxon_name_ids

        if p.blank? && s.empty? #.nil?
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb and 1 other location - About 25 mins to fix
            lib/queries/biological_association/filter.rb on lines 401..412

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 29.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                  def subject_otu_query
        p = otu_params
        s = subject_taxon_name_ids

        if p.blank? && s.nil?
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb and 1 other location - About 20 mins to fix
            lib/queries/biological_association/filter.rb on lines 429..440

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 28.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                  def object_otu_query
        p = otu_params
        s = object_taxon_name_ids

        if p.blank? && s.nil?
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb and 1 other location - About 20 mins to fix
            lib/queries/biological_association/filter.rb on lines 415..426

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 28.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Re-enable Metrics/MethodLength cop with # rubocop:enable after disabling it.
            Open

                  # rubocop:disable Metrics/MethodLength
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb by rubocop

            Freeze mutable objects assigned to constants.
            Open

                  API_PARAM_EXCLUSIONS = [
        :any_global_id
      ]
            Severity: Minor
            Found in lib/queries/biological_association/filter.rb by rubocop

            This cop checks whether some constant value isn't a mutable literal (e.g. array or hash).

            Strict mode can be used to freeze all constants, rather than just literals. Strict mode is considered an experimental feature. It has not been updated with an exhaustive list of all methods that will produce frozen objects so there is a decent chance of getting some false positives. Luckily, there is no harm in freezing an already frozen object.

            Example: EnforcedStyle: literals (default)

            # bad
CONST = [1, 2, 3]

# good
CONST = [1, 2, 3].freeze

# good
CONST = <<~TESTING.freeze
  This is a heredoc
TESTING

# good
CONST = Something.new

            Example: EnforcedStyle: strict

            # bad
CONST = Something.new

# bad
CONST = Struct.new do
  def foo
    puts 1
  end
end

# good
CONST = Something.new.freeze

# good
CONST = Struct.new do
  def foo
    puts 1
  end
end.freeze

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